# ./galigner /home/luo_group/data/human_ref/ref_good/ref_good.fa.index /home/luo_group/data/human_reads/SRR001258_35bp_1M.fasta output
#36 bp
#time ./galigner /home/lumian/data/human_ref/soap3-index/hg19.fa.index /home/lumian/data/human_reads/SRR003084_1M_new.fasta output
#50 bp
#time ./galigner /home/lumian/data/human_ref/soap3-index/hg19.fa.index /home/lumian/data/human_reads/SRR003092_1M.fasta ./output
#67 bp
#time ./galigner /home/luo_group/data/human_ref/ref_good/ref_good.fa.index /home/luo_group/data/human_reads/sequence/sequence/SRR073318_1M.fasta output -nc

#time ./galigner /home/luo_group/data/human_ref/ref_good/ref_good.fa.index /home/luo_group/data/human_reads/sequence/sequence/SRR003092_1M.fasta output -nc 

#time ./galigner /home/luo_group/data/human_ref/ref_good/ref_good.fa.index /home/luo_group/data/human_reads/sequence/sequence/SRR003092_1M.fasta output -nc

#chr1_1M
time ./galigner /home/luo_group/data/snp_data/human/hg18_ref/soap3/chr1_good.fa.index /lhome/mian/data/chr1_1M.fastq output -nc 

#chr1_15M
#time ./galigner /home/luo_group/data/snp_data/human/hg18_ref/soap3/chr1_good.fa.index /lhome/mian/data/chr1_15M.fastq output -nc
